Fitting a linear model using limma

Usage

perform_limma(
  data,
  condition_vector,
  comparisons,
  covariate = NULL,
  trend = TRUE,
  robust = TRUE
)

data: Data table of intensities (rows = proteins, cols = samples)
condition_vector: Vector of experimental design specifying the condition(s) to compare
comparisons: Vector of comparisons that are performed in the DE analysis (from specify_comparisons method)
covariate: String specifying which column to include as covariate into limma
trend: logical, should an intensity-dependent trend be allowed for the prior variance? If FALSE then the prior variance is constant. Alternatively, trend can be a row-wise numeric vector, which will be used as the covariate for the prior variance.
robust: logical, should the estimation of df.prior and var.prior be robustified against outlier sample variances?

eBayes object